SMTL ID : 2px4.1

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: Y.119, R.265, A.266 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: G.51, G.52, N.259, L.260, G.261 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: G.148, E.149, R.160 Ligand excluded by PLIP

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: R.37, R.41, V.55, S.56, R.57, R.84 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.55, A:R.57 Salt bridges: A:R.37, A:R.41, A:R.57, A:R.84 SO4.5: 8 residues within 4Å: Chain A: R.57, K.61, L.211, S.212, R.213, N.216, E.218 Ligands: SO4.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.213, A:N.216 Water bridges: A:R.57, A:E.218 Salt bridges: A:R.57, A:K.61, A:R.213 SO4.6: 4 residues within 4Å: Chain A: R.63, D.257, V.258, N.259 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.259, A:N.259 Water bridges: A:R.63, A:R.63 Salt bridges: A:R.63 SO4.7: 3 residues within 4Å: Chain A: G.203, G.204, S.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.204, A:S.223 SO4.8: 2 residues within 4Å: Chain A: A.31, R.243 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.243 SO4.9: 5 residues within 4Å: Chain A: F.24, R.28, R.213, S.215 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.215 Salt bridges: A:R.28, A:R.213 SO4.10: 3 residues within 4Å: Chain A: R.84, E.111, E.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.112 Water bridges: A:H.110 Salt bridges: A:R.84

9 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.11: 4 residues within 4Å: Chain A: D.170 Ligands: UNX.12, UNX.13, UNX.16 No protein-ligand interaction detected (PLIP) UNX.12: 7 residues within 4Å: Chain A: S.137, M.167, D.170, W.171 Ligands: UNX.11, UNX.13, UNX.16 No protein-ligand interaction detected (PLIP) UNX.13: 5 residues within 4Å: Chain A: S.137, D.170 Ligands: UNX.11, UNX.12, UNX.14 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain A: P.136, S.137 Ligands: UNX.13 No protein-ligand interaction detected (PLIP) UNX.15: 4 residues within 4Å: Chain A: F.133 Ligands: UNX.17, UNX.18, UNX.19 No protein-ligand interaction detected (PLIP) UNX.16: 5 residues within 4Å: Chain A: M.167, D.170 Ligands: UNX.11, UNX.12, UNX.19 No protein-ligand interaction detected (PLIP) UNX.17: 2 residues within 4Å: Chain A: F.133 Ligands: UNX.15 No protein-ligand interaction detected (PLIP) UNX.18: 3 residues within 4Å: Chain A: R.163 Ligands: UNX.15, UNX.19 No protein-ligand interaction detected (PLIP) UNX.19: 4 residues within 4Å: Chain A: F.133 Ligands: UNX.15, UNX.16, UNX.18 No protein-ligand interaction detected (PLIP)

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.20: 18 residues within 4Å: Chain A: S.56, G.58, T.59, G.81, C.82, G.83, G.86, W.87, T.104, K.105, H.110, E.111, V.130, D.131, V.132, F.133, D.146, I.147 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.56, A:C.82, A:G.85, A:G.86, A:W.87, A:W.87, A:T.104, A:K.105, A:E.111, A:D.131, A:V.132, A:D.146 Water bridges: A:S.88, A:E.111, A:E.111, A:G.148 pi-Cation interactions: A:K.105

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 1 residues within 4Å: Chain A: S.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.173, A:S.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Assenberg, R. et al., Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues. J.Gen.Virol. (2007)

Release Date

2007-05-29

Peptides

Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]

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